Dynamic conformational states of apo, ATP and cabozantinib bound TAM kinases to differentiate active-inactive kinetic models

Abstract

The dynamically active and inactive conformations of kinases play a crucial role in the activation of intracellular downstream signaling pathways. The all-atom molecular dynamics (MD) simulations at microsecond (µs) timescale and longer provide robust insights into the structural details of conformational alterations in kinases that contribute to their cellular metabolic activities and signaling pathways. Tyro3, Axl and Mer (TAM) receptor tyrosine kinases (RTKs) are overexpressed in several types of human cancers. Cabozantinib, a small molecule inhibitor constrains the activity of TAM kinases at nanomolar concentrations. The apo, complexes of ATP (active state) and cabozantinib (active and inactive states) with TAM RTKs were studied by 1 µs MD simulations followed by trajectory analyses. The dynamic mechanistic pathways intrinsic to the kinase activity and protein conformational landscape in the cabozantinib bound TAM kinases are revealed due to the alterations in the P-loop, α-helix and activation loop that result in breaking the regulatory (R) and catalytic (C) spines, while the active states of ATP bound TAM kinases are retained. The co-existence of dynamical states when bound to cabozantinib was observed and the long-lived kinetic transition states of distinct active and inactive structural models were deciphered from MD simulation trajectories that have not been revealed so far.

Communicated by Ramaswamy H. Sarma

KEYWORDS:

• Active and inactive states
• ATP
• cabozantinib
• catalytic spine
• kinetic equilibrium metastable states
• kinetic transition states
• Markov state models
• molecular dynamics simulations
• principal component analysis
• regulatory spine
• Tyro3
• Axl and Mer kinases

Author contributions

Naresh GKRS carried out the research work, methodologies and wrote the manuscript. Lalitha Guruprasad conceived the idea, supervised and wrote the manuscript.

Disclosure statement

The authors declare no competing interests.

Data availability statement

All 12 µs MD structures and trajectory data, Markov models are available upon reasonable request to corresponding author ([email protected]). The rest of the all data held with manuscript supporting information including videos.

Additional information

Funding

NGKRS thanks University of Hyderabad for UGC Non-NET fellowship. The authors thanks DST-PURSE and UGC UPE2 for funding and CMSD for computational facilities.